Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001854.1 Hibiscus syriacus cultivar Beakdansim tig00003754_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 54130
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2079 original size:25 final size:26
Alignment explanation
Indices: 2041--2089 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2031 ACACTTTAAA
*
2041 TAATTTTTAATTTATAAA-TAAAAACT
1 TAATTATTAATTTA-AAATTAAAAACT
2067 TAATTATT-ATTTAAAATTAAAAA
1 TAATTATTAATTTAAAATTAAAAA
2090 AATATTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 11 0.52
26 7 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTATTAATTTAAAATTAAAAACT
Found at i:2160 original size:53 final size:54
Alignment explanation
Indices: 2102--2218 Score: 166
Period size: 53 Copynumber: 2.2 Consensus size: 54
2092 TATTCAAGAA
*
2102 CCAAATTGCATATCAAAATTAAAGTCAACGCCAAATTGCACT-AAAAA-AGGGAT
1 CCAAATTGCATATAAAAATTAAAGTCAACGCCAAATTGCACTAAAAAATAGGG-T
*** *
2155 CCAAATTGCATATAAAAATTAAAGTCGGTGCCAAATTGCATTAAAAAATAGGGT
1 CCAAATTGCATATAAAAATTAAAGTCAACGCCAAATTGCACTAAAAAATAGGGT
2209 CCAAATTGCA
1 CCAAATTGCA
2219 AAGTTAGGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
53 37 0.65
54 16 0.28
55 4 0.07
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (54 bp):
CCAAATTGCATATAAAAATTAAAGTCAACGCCAAATTGCACTAAAAAATAGGGT
Found at i:2761 original size:3 final size:3
Alignment explanation
Indices: 2753--2781 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2743 ACAACAGGTA
2753 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2782 CTCAAATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:11251 original size:14 final size:14
Alignment explanation
Indices: 11214--11258 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
11204 TCATATCAAC
11214 AAATGAATTTACA-
1 AAATGAATTTACAT
* *
11227 CAATAAATTTACAT
1 AAATGAATTTACAT
11241 AAATGAATTTACAT
1 AAATGAATTTACAT
11255 AAAT
1 AAAT
11259 ATTTTATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (14 bp):
AAATGAATTTACAT
Found at i:11440 original size:14 final size:14
Alignment explanation
Indices: 11421--11449 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11411 TATATTTATT
11421 CCTTCGATTAATAA
1 CCTTCGATTAATAA
11435 CCTTCGATTAATAA
1 CCTTCGATTAATAA
11449 C
1 C
11450 AACATGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (14 bp):
CCTTCGATTAATAA
Found at i:23173 original size:24 final size:24
Alignment explanation
Indices: 23137--23207 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
23127 ACCATATTTG
* *
23137 TTCTACTAGCTTATGAATAATCAA
1 TTCTACCAACTTATGAATAATCAA
*
23161 TTCTTCCAACTTATGAATAATCAA
1 TTCTACCAACTTATGAATAATCAA
*
23185 TTCTACCAACTTACGAATAATCA
1 TTCTACCAACTTATGAATAATCA
23208 TCCTTATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (24 bp):
TTCTACCAACTTATGAATAATCAA
Found at i:38279 original size:50 final size:51
Alignment explanation
Indices: 38181--38285 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 51
38171 ACGAGCCGGG
38181 TTCTAATTGGTCCAAATACTAGTAAATCTTCCTTTTCATATGTATGTCCTT
1 TTCTAATTGGTCCAAATACTAGTAAATCTTCCTTTTCATATGTATGTCCTT
38232 TTCTAATTGGTCCAAATACTAGT-AATCTTCCTTTTCATATGTATGTCCTT
1 TTCTAATTGGTCCAAATACTAGTAAATCTTCCTTTTCATATGTATGTCCTT
38282 TTCT
1 TTCT
38286 TTATTTCTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 31 0.57
51 23 0.43
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.47
Consensus pattern (51 bp):
TTCTAATTGGTCCAAATACTAGTAAATCTTCCTTTTCATATGTATGTCCTT
Found at i:47513 original size:23 final size:24
Alignment explanation
Indices: 47487--47537 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
47477 ACTTTATTAT
*
47487 TTTAATAT-ATACTTTTAATAAAA
1 TTTAATATAAAACTTTTAATAAAA
* *
47510 TTT-ATATAAAATTTTTTATAAAA
1 TTTAATATAAAACTTTTAATAAAA
47533 TTTAA
1 TTTAA
47538 AAGATAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 18 0.78
24 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAATATAAAACTTTTAATAAAA
Done.